S-Store: Streaming Meets Transaction Processing

Stream processing addresses the needs of real-time applications. Transaction processing addresses the coordination and safety of short atomic computations. Heretofore, these two modes of operation existed in separate, stove-piped systems. In this work, we attempt to fuse the two computational paradigms in a single system called S-Store. In this way, S-Store can simultaneously accommodate OLTP and streaming applications. We present a simple transaction model for streams that integrates seamlessly with a traditional OLTP system. We chose to build S-Store as an extension of H-Store, an open-source, in-memory, distributed OLTP database system. By implementing S-Store in this way, we can make use of the transaction processing facilities that H-Store already supports, and we can concentrate on the additional implementation features that are needed to support streaming. Similar implementations could be done using other main-memory OLTP platforms. We show that we can actually achieve higher throughput for streaming workloads in S-Store than an equivalent deployment in H-Store alone. We also show how this can be achieved within H-Store with the addition of a modest amount of new functionality. Furthermore, we compare S-Store to two state-of-the-art streaming systems, Spark Streaming and Storm, and show how S-Store matches and sometimes exceeds their performance while providing stronger transactional guarantees

Collaborative Reuse of Streaming Dataflows in IoT Applications

Distributed Stream Processing Systems (DSPS) like Apache Storm and Spark Streaming enable composition of continuous dataflows that execute persistently over data streams. They are used by Internet of Things (IoT) applications to analyze sensor data from Smart City cyber-infrastructure, and make active utility management decisions. As the ecosystem of such IoT applications that leverage shared urban sensor streams continue to grow, applications will perform duplicate pre-processing and analytics tasks. This offers the opportunity to collaboratively reuse the outputs of overlapping dataflows, thereby improving the resource efficiency. In this paper, we propose \emph{dataflow reuse algorithms} that given a submitted dataflow, identifies the intersection of reusable tasks and streams from a collection of running dataflows to form a \emph{merged dataflow}. Similar algorithms to unmerge dataflows when they are removed are also proposed. We implement these algorithms for the popular Apache Storm DSPS, and validate their performance and resource savings for 35 synthetic dataflows based on public OPMW workflows with diverse arrival and departure distributions, and on 21 real IoT dataflows from RIoTBench.Comment: To appear in IEEE eScience Conference 201

FAST: FAST Analysis of Sequences Toolbox.

FAST (FAST Analysis of Sequences Toolbox) provides simple, powerful open source command-line tools to filter, transform, annotate and analyze biological sequence data. Modeled after the GNU (GNU's Not Unix) Textutils such as grep, cut, and tr, FAST tools such as fasgrep, fascut, and fastr make it easy to rapidly prototype expressive bioinformatic workflows in a compact and generic command vocabulary. Compact combinatorial encoding of data workflows with FAST commands can simplify the documentation and reproducibility of bioinformatic protocols, supporting better transparency in biological data science. Interface self-consistency and conformity with conventions of GNU, Matlab, Perl, BioPerl, R, and GenBank help make FAST easy and rewarding to learn. FAST automates numerical, taxonomic, and text-based sorting, selection and transformation of sequence records and alignment sites based on content, index ranges, descriptive tags, annotated features, and in-line calculated analytics, including composition and codon usage. Automated content- and feature-based extraction of sites and support for molecular population genetic statistics make FAST useful for molecular evolutionary analysis. FAST is portable, easy to install and secure thanks to the relative maturity of its Perl and BioPerl foundations, with stable releases posted to CPAN. Development as well as a publicly accessible Cookbook and Wiki are available on the FAST GitHub repository at https://github.com/tlawrence3/FAST. The default data exchange format in FAST is Multi-FastA (specifically, a restriction of BioPerl FastA format). Sanger and Illumina 1.8+ FastQ formatted files are also supported. FAST makes it easier for non-programmer biologists to interactively investigate and control biological data at the speed of thought

Complex Actions for Event Processing

Automatic reactions triggered by complex events have been deployed with great success in particular domains, among others, in algorithmic trading, the automatic reaction to realtime analysis of marked data. However, to date, reactions in complex event processing systems are often still limited to mere modifications of internal databases or are realized by means similar to remote procedure calls. In this paper, we argue that expressive complex actions with support for composite work ows and integration of so called external actions are desirable for a wide range of real-world applications among other emergency management. This article investigates the particularities of external actions needed in emergency management, which are initiated inside the event processing system but which are actually executed by external actuators, and discuss the implications of these particularities on composite actions. Based on these observations, we propose versatile complex actions with temporal dependencies and a seamless integration of complex events and external actions. This article also investigates how the proposed integrated approach towards complex events and complex actions can be evaluated based on simple reactive rules. Finally, it is shown how complex actions can be deployed for a complex event processing system devoted to emergency management

Building trainable taggers in a web-based, UIMA-supported NLP workbench

Argo is a web-based NLP and text mining workbench with a convenient graphical user interface for designing and executing processing workflows of various complexity. The workbench is intended for specialists and nontechnical audiences alike, and provides the ever expanding library of analytics compliant with the Unstructured Information Management Architecture, a widely adopted interoperability framework. We explore the flexibility of this framework by demonstrating workflows involving three processing components capable of performing self-contained machine learning-based tagging. The three components are responsible for the three distinct tasks of 1) generating observations or features, 2) training a statistical model based on the generated features, and 3) tagging unlabelled data with the model. The learning and tagging components are based on an implementation of conditional random fields (CRF); whereas the feature generation component is an analytic capable of extending basic token information to a comprehensive set of features. Users define the features of their choice directly from Argo’s graphical interface, without resorting to programming (a commonly used approach to feature engineering). The experimental results performed on two tagging tasks, chunking and named entity recognition, showed that a tagger with a generic set of features built in Argo is capable of competing with taskspecific solutions.

Distributed Holistic Clustering on Linked Data

Link discovery is an active field of research to support data integration in the Web of Data. Due to the huge size and number of available data sources, efficient and effective link discovery is a very challenging task. Common pairwise link discovery approaches do not scale to many sources with very large entity sets. We here propose a distributed holistic approach to link many data sources based on a clustering of entities that represent the same real-world object. Our clustering approach provides a compact and fused representation of entities, and can identify errors in existing links as well as many new links. We support a distributed execution of the clustering approach to achieve faster execution times and scalability for large real-world data sets. We provide a novel gold standard for multi-source clustering, and evaluate our methods with respect to effectiveness and efficiency for large data sets from the geographic and music domains